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- PDB-3k6u: M. acetivorans Molybdate-Binding Protein (ModA) in Unliganded Ope... -

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Basic information

Entry
Database: PDB / ID: 3k6u
TitleM. acetivorans Molybdate-Binding Protein (ModA) in Unliganded Open Form
ComponentsSolute-binding protein MA_0280
KeywordsTRANSPORT PROTEIN / ModA / molybdate / Methanosarcina acetivorans / periplasmic binding protein / ABC transporter / ligand / metal-binding protein
Function / homologyTungstate ABC transporter, substrate-binding protein WtpA / tungstate binding / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized solute-binding protein MA_0280
Function and homology information
Biological speciesMethanosarcina acetivorans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.95 Å
AuthorsChan, S. / Giuroiu, I. / Chernishof, I. / Sawaya, M.R. / Chiang, J. / Gunsalus, R.P. / Arbing, M.A. / Perry, L.J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Apo and ligand-bound structures of ModA from the archaeon Methanosarcina acetivorans
Authors: Chan, S. / Giuroiu, I. / Chernishof, I. / Sawaya, M.R. / Chiang, J. / Gunsalus, R.P. / Arbing, M.A. / Perry, L.J.
History
DepositionOct 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 21, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Solute-binding protein MA_0280


Theoretical massNumber of molelcules
Total (without water)39,1601
Polymers39,1601
Non-polymers00
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.179, 82.179, 104.940
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Solute-binding protein MA_0280


Mass: 39160.156 Da / Num. of mol.: 1 / Fragment: UNP residues 27 to 352
Source method: isolated from a genetically manipulated source
Details: N-terminal TEV-cleavable 6xHis-tag / Source: (gene. exp.) Methanosarcina acetivorans (archaea) / Strain: C2A / Gene: MA0280, MA_0280 / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: Q8TTZ5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.6152.91
2
3
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, sitting drop6.41.4M tri-Ammonium Citrate, p6.4, vapor diffusion, sitting drop, temperature 293K
2932vapor diffusion, sitting drop6.41.6M tri-Ammonium Citrate, p6.4, soaked in 0.5M potassium iodide for 30 seconds, vapor diffusion, sitting drop, temperature 293K
2933vapor diffusion, sitting drop6.41.6M tri-Ammonium Citrate, p6.4, soaked in 1M cesium chloride for 18 minutes, vapor diffusion, sitting drop, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
1,2,31
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONALS 8.2.210.954
SYNCHROTRONALS 8.2.221.459
ROTATING ANODEOTHER31.542
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDNov 21, 2004
ADSC QUANTUM 3152CCDNov 21, 2004
RIGAKU RAXIS IV++3IMAGE PLATENov 23, 2004
Radiation
IDProtocolScattering typeWavelength-ID
1SINGLE WAVELENGTHx-ray1
2SINGLE WAVELENGTHx-ray1
3SINGLE WAVELENGTHx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9541
21.4591
31.5421
ReflectionAv σ(I) over netI: 22.45 / Number: 195952 / Rmerge(I) obs: 0.124 / Χ2: 1 / D res high: 2.7 Å / D res low: 90 Å / Num. obs: 21339 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
5.829099.710.0540.994
4.625.8210010.0781.001
4.034.6210010.0930.994
3.664.0310010.1130.997
3.43.6610010.1431.008
3.23.410010.191.007
3.043.210010.2871.001
2.913.0499.910.3631.008
2.82.9110010.4930.995
2.72.810010.5880.995
ReflectionResolution: 1.94→38.26 Å / Num. obs: 29447 / % possible obs: 99.9 % / Redundancy: 10.86 % / Rmerge(I) obs: 0.092 / Rsym value: 0.079 / Χ2: 1.03 / Net I/σ(I): 18.6
Reflection shellResolution: 1.94→2.01 Å / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 10.43 / Num. unique all: 2936 / Rsym value: 0.468 / Χ2: 1.021 / % possible all: 100

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Phasing

PhasingMethod: MIRAS
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 29027
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.42-10051.70.833503
5.96-7.4253.60.834516
5.19-5.9653.30.841525
4.66-5.1950.70.854603
4.26-4.66560.835646
3.95-4.2657.10.813713
3.7-3.9559.10.79744
3.49-3.762.90.788823
3.32-3.4961.70.765839
3.17-3.3268.30.741896
3.03-3.1769.60.755931
2.92-3.0369.20.721979
2.81-2.9266.90.6961015
2.72-2.8175.40.6041028
2.63-2.7289.90.4861090
2.55-2.6390.20.4891120
2.48-2.5587.80.5381135
2.42-2.4889.30.5481187
2.35-2.42910.5551214
2.3-2.3588.80.5421248
2.25-2.3900.5471272
2.2-2.2589.30.4981308
2.15-2.288.80.5591282
2.11-2.1588.20.5511372
2.07-2.1190.70.561401
2.03-2.07930.5281404
1.99-2.0388.10.5411413
1.95-1.9989.80.5011820
Phasing MIRResolution: 1.95→20 Å / FOM: 0.368 / FOM acentric: 0.363 / FOM centric: 0.513 / Reflection: 10848 / Reflection acentric: 10438 / Reflection centric: 410
Phasing MIR der

Der set-ID: 1

IDResolution (Å)R cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
11.95-200.830.845983.71.220.8910438410
21.95-200.980.9871.893.10.250.227253319
iodide
Cesium
Phasing MIR der shell
Highest resolution (Å)Lowest resolution (Å)Der-IDR cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
9.2720iodide0.851.2968112.62.271.2123932
6.039.27iodide0.740.9753.4932.391.3467348
4.476.03iodide0.770.7159.881.11.751.07137969
3.554.47iodide0.840.8276.597.61.030.74231384
2.953.55iodide0.840.7958.478.80.970.663508111
2.522.95iodide0.850.8342.856.21.020.68232666
2.22.52iodide00000000
1.952.2iodide00000000
9.2720Cesium0.920.9369.191.10.730.4623930
6.039.27Cesium0.90.9146.270.40.820.4667348
4.476.03Cesium0.970.9762.685.80.410.28137969
3.554.47Cesium0.991.0183.9100.70.180.15231384
2.953.55Cesium10.9972.7104.60.120.09264988
2.522.95Cesium00000000
2.22.52Cesium00000000
1.952.2Cesium00000000
Phasing MIR der site
IDDer-IDBiso (Å)Atom type symbolFract xFract yFract zOccupancy
1iodide25.663I-0.4980.130.0210.71
2iodide38.498I-0.2860.3390.0950.542
3iodide41.684I-0.2970.5340.0990.542
4iodide42.947I-0.1860.160.1440.518
5iodide42.946I-0.9260.5430.0510.507
6iodide45.642I-0.0410.5370.0260.451
7Cesium76.553Cs0.0790.2430.2260.412
8Cesium64.82Cs0.6550.5950.0480.25
Phasing MIR shell
Resolution (Å)FOMFOM acentricFOM centricReflectionReflection acentricReflection centric
9.27-200.6130.6050.67327123932
6.03-9.270.6220.6180.67972167348
4.47-6.030.5110.5050.6171448137969
3.55-4.470.3540.350.4792397231384
2.95-3.550.3090.3050.4436193508111
2.52-2.950.2830.280.3692392232666
2.2-2.5200000
1.95-2.200000

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM5phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MIRAS / Resolution: 1.95→38.26 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.234 / WRfactor Rwork: 0.197 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.87 / SU B: 6.561 / SU ML: 0.086 / SU R Cruickshank DPI: 0.136 / SU Rfree: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1453 5 %RANDOM
Rwork0.177 ---
obs0.178 29271 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 54.9 Å2 / Biso mean: 17.613 Å2 / Biso min: 5.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20.46 Å20 Å2
2--0.93 Å20 Å2
3----1.39 Å2
Refinement stepCycle: LAST / Resolution: 1.95→38.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2423 0 0 176 2599
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222493
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.9673401
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9825313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17626125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49715403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.826159
X-RAY DIFFRACTIONr_chiral_restr0.1080.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211941
X-RAY DIFFRACTIONr_mcbond_it0.8831.51561
X-RAY DIFFRACTIONr_mcangle_it1.6422528
X-RAY DIFFRACTIONr_scbond_it2.6133932
X-RAY DIFFRACTIONr_scangle_it4.3184.5872
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 106 -
Rwork0.211 2031 -
all-2137 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 15.8757 Å / Origin y: 25.8208 Å / Origin z: 14.2498 Å
111213212223313233
T0.0437 Å20.0162 Å2-0.0005 Å2-0.023 Å2-0.0007 Å2--0.0637 Å2
L1.4481 °2-0.2859 °2-1.8669 °2-0.5945 °20.1416 °2--3.363 °2
S-0.0637 Å °-0.0434 Å °-0.0352 Å °0.0472 Å °0.0116 Å °0.0301 Å °0.2449 Å °0.0923 Å °0.0521 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 201
2X-RAY DIFFRACTION1A203 - 354

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